title: Comparison of correspondence analysis methods for synonymous codon usage in bacteria.
abstract: Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.
authors.affiliation: Department of Biological Sciences and Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, PO Box 443051, Moscow, Idaho 83844-3051, USA. hsuzuki@uidaho.edu
authors.forename: Haruo
authors.initials: H
authors.lastname: Suzuki
authors.forename: Celeste J
authors.initials: CJ
authors.lastname: Brown
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Forney
authors.forename: Eva M
authors.initials: EM
authors.lastname: Top
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D001482:Base Composition; D003062:Codon / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D005815:Genetic Code; D005821:Genetic Techniques; D016680:Genome, Bacterial; D012283:Rickettsia prowazekii
chemical_list: D003062:Codon